On 2010-04-04 06.40, Chih-Ying Lin wrote:
HI
1. dssp -n index.ndx
=> only atom numbers of one residue in the index.ndx
=> can dssp decide the exact second structure for the only one residue
without considering other residues of protein?
no.
=> can i get the same second structure for the residue with [ dssp -n
one-residue.ndx ] and [dssp -n protein-main chain + H .ndx ] ?
no.
2. The legend indicates the color of different second structure is shown
under the secondary-structure plot.
I don't want to change the colors assigned, but one legend is
half-shown. The picture of legend is cut.
How can I get that legend full-shown.
send your command lines.
3. With the option
-sss string HE
HE = helix ?
no, this is DSSP coding. H = helix , E = extended (Beta sheet), B = beta
turn, T = som other kind of turn, 3 = 3-10 heix, 5 = pi helix.
Thanks
Lin
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
